2 Laboratory performance

2.1 Load data

Load data previously compiled from the database:

all_data <- read_tsv("data/all_data.tsv")

2.2 DNA yield

Total amount of DNA extracted from the 150 ul subset of the bead-beaten sample.

all_data %>%
    group_by(Taxon,Extraction) %>%
    summarise(value = sprintf("%.0f±%.0f", mean(extract), sd(extract))) %>%
    pivot_wider(names_from = Extraction, values_from = value) %>%
    tt(caption = "Mean and standard deviation of total DNA nanograms")
tinytable_28a74i0azlc5qs0fzoju
Mean and standard deviation of total DNA nanograms
Taxon DREX EHEX ZYMO
Amphibian 482±546 1733±1145 471±347
Bird 13±12 54±45 73±127
Control 2±3 1±0 0±0
Mammal 265±214 904±672 445±394
Reptile 162±128 250±171 102±68 
all_data %>%
    ggplot(aes(x=Extraction,y=extract))+ 
        geom_boxplot() + 
        facet_grid(. ~ Taxon, scales = "free") +
        labs(y="DNA yield (ng)",x="Extraction method")

all_data  %>%
    filter(Taxon != "Control") %>%
    lmerTest::lmer(extract ~ Extraction + (1 | Sample) + (1 | Species), data = ., REML = FALSE) %>%
    broom.mixed::tidy() %>%
    tt()
tinytable_lgdbg7uvb39s4yilzgk8
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) 120.70599 125.49705 0.9618233 16.14808 3.503209e-01
fixed NA ExtractionEHEX 620.27971 74.78157 8.2945532 153.30986 5.196360e-14
fixed NA ExtractionZYMO 39.65796 74.42689 0.5328445 153.24421 5.949131e-01
ran_pars Sample sd__(Intercept) 164.00812 NA NA NA NA
ran_pars Species sd__(Intercept) 374.85139 NA NA NA NA
ran_pars Residual sd__Observation 400.80106 NA NA NA NA

2.3 Library performance

Number of PCR cycles required for reaching the plateau phase of the indexing PCR.

all_data %>%
    group_by(Taxon,Extraction) %>%
    summarise(value = sprintf("%.1f±%.1f", mean(pcr), sd(pcr))) %>%
    pivot_wider(names_from = Extraction, values_from = value) %>%
    tt(caption = "Mean and standard deviation of optimal number of PCR cycles")
tinytable_v5jij3i7f545nfjjfbc2
Mean and standard deviation of optimal number of PCR cycles
Taxon DREX EHEX ZYMO
Amphibian 10.7±2.9 10.7±2.3 14.3±1.6
Bird 18.7±4.3 14.4±2.3 17.6±2.8
Control 19.8±0.5 22.0±4.2 20.0±2.8
Mammal 9.9±1.9 10.0±2.1 11.1±3.5
Reptile 10.3±3.5 12.0±3.3 11.7±4.0 
all_data %>%
    ggplot(aes(x=Extraction,y=pcr))+ 
        geom_boxplot() + 
        facet_grid(. ~ Taxon, scales = "free") +
        labs(y="Optimal number of PCR cycles",x="Extraction method")

all_data  %>%
    filter(Taxon != "Control") %>%
    lmerTest::lmer(pcr ~ Extraction + (1 | Sample) + (1 | Species), data = ., REML = FALSE) %>%
    broom.mixed::tidy() %>%
    tt()
tinytable_6pvfvctr7us0hgsivgdj
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) 12.2930699 0.8648942 14.213380 14.90821 4.500117e-10
fixed NA ExtractionEHEX -0.5222953 0.5130831 -1.017955 150.84234 3.103294e-01
fixed NA ExtractionZYMO 1.5689655 0.5106532 3.072468 150.76244 2.519836e-03
ran_pars Sample sd__(Intercept) 1.0689643 NA NA NA NA
ran_pars Species sd__(Intercept) 2.5992293 NA NA NA NA
ran_pars Residual sd__Observation 2.7499517 NA NA NA NA